7A5V

CryoEM structure of a human gamma-aminobutyric acid receptor, the GABA(A)R-beta3 homopentamer, in complex with histamine and megabody Mb25 in lipid nanodisc


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Single-particle cryo-EM at atomic resolution.

Nakane, T.Kotecha, A.Sente, A.McMullan, G.Masiulis, S.Brown, P.M.G.E.Grigoras, I.T.Malinauskaite, L.Malinauskas, T.Miehling, J.Uchanski, T.Yu, L.Karia, D.Pechnikova, E.V.de Jong, E.Keizer, J.Bischoff, M.McCormack, J.Tiemeijer, P.Hardwick, S.W.Chirgadze, D.Y.Murshudov, G.Aricescu, A.R.Scheres, S.H.W.

(2020) Nature 587: 152-156

  • DOI: 10.1038/s41586-020-2829-0
  • Primary Citation of Related Structures:  
    7A4M, 7A5V

  • PubMed Abstract: 
  • The three-dimensional positions of atoms in protein molecules define their structure and their roles in biological processes. The more precisely atomic coordinates are determined, the more chemical information can be derived and the more mechanistic insi ...

    The three-dimensional positions of atoms in protein molecules define their structure and their roles in biological processes. The more precisely atomic coordinates are determined, the more chemical information can be derived and the more mechanistic insights into protein function may be inferred. Electron cryo-microscopy (cryo-EM) single-particle analysis has yielded protein structures with increasing levels of detail in recent years 1,2 . However, it has proved difficult to obtain cryo-EM reconstructions with sufficient resolution to visualize individual atoms in proteins. Here we use a new electron source, energy filter and camera to obtain a 1.7 Å resolution cryo-EM reconstruction for a human membrane protein, the β3 GABA A receptor homopentamer 3 . Such maps allow a detailed understanding of small-molecule coordination, visualization of solvent molecules and alternative conformations for multiple amino acids, and unambiguous building of ordered acidic side chains and glycans. Applied to mouse apoferritin, our strategy led to a 1.22 Å resolution reconstruction that offers a genuine atomic-resolution view of a protein molecule using single-particle cryo-EM. Moreover, the scattering potential from many hydrogen atoms can be visualized in difference maps, allowing a direct analysis of hydrogen-bonding networks. Our technological advances, combined with further approaches to accelerate data acquisition and improve sample quality, provide a route towards routine application of cryo-EM in high-throughput screening of small molecule modulators and structure-based drug discovery.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, UK. scheres@mrc-lmb.cam.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit beta-3 A396Homo sapiensMutation(s): 0 
Gene Names: GABRB3
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Cys-Loop Receptor Family
Protein: 
GABAA receptor (β3 homopentamer) in complex with histamine and megabody Mb25 in lipid nanodisc
Find proteins for P28472 (Homo sapiens)
Explore P28472 
Go to UniProtKB:  P28472
NIH Common Fund Data Resources
PHAROS:  P28472
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Megabody Mb25 O522Lama glamaMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2 N-Glycosylation Oligosaccharides Interaction
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
5 N-Glycosylation Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_UP_A025_1012
Medical Research Council (MRC, United Kingdom)United KingdomMR/L009609/1
Medical Research Council (MRC, United Kingdom)United KingdomMC_UP_1201/15
Medical Research Council (MRC, United Kingdom)United KingdomMC_UP_A025_1013
Wellcome TrustUnited Kingdom206171/Z/17/Z
Wellcome TrustUnited Kingdom202905/Z/16/Z)

Revision History 

  • Version 1.0: 2020-11-18
    Type: Initial release
  • Version 1.1: 2020-11-25
    Changes: Database references